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- PDB-4ewc: Crystal Structure of the Infectious Salmon Anemia Virus Nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 4ewc
TitleCrystal Structure of the Infectious Salmon Anemia Virus Nucleoprotein
ComponentsPutative nucleoprotein
KeywordsRNA BINDING PROTEIN / Alpha-helical / RNA encapsidation / isavirus / orthomyoxovirus / nucleoprotein / NP / RNA binding / replication / transcription / viral RNA packaging
Function / homology
Function and homology information


host cell nucleolus / helical viral capsid / viral penetration into host nucleus / viral nucleocapsid / membrane => GO:0016020 / symbiont entry into host cell
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1660 / N-terminal domain of TfIIb - #560 / N-terminal domain of TfIIb / Single Sheet / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Nucleoprotein / Putative nucleoprotein
Similarity search - Component
Biological speciesInfectious salmon anemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsZheng, W. / Tao, Y.J.
CitationJournal: Plos Pathog. / Year: 2013
Title: The crystal structure and RNA-binding of an orthomyxovirus nucleoprotein.
Authors: Zheng, W. / Olson, J. / Vakharia, V. / Tao, Y.J.
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative nucleoprotein


Theoretical massNumber of molelcules
Total (without water)68,3141
Polymers68,3141
Non-polymers00
Water77543
1
A: Putative nucleoprotein

A: Putative nucleoprotein


Theoretical massNumber of molelcules
Total (without water)136,6272
Polymers136,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area7020 Å2
ΔGint-48 kcal/mol
Surface area40530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.983, 112.983, 103.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Putative nucleoprotein


Mass: 68313.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious salmon anemia virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q91BR3, UniProt: Q8V3T7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE CORRESPONDS TO THE GENEBANK ENTRY JX070881

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 4
Details: 20% PEG6000, 0.8M Lithium Chloride, 0.1M Sodium Citrate, pH 4.0, VAPOR DIFFUSION, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97895 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 1, 2011
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 18991 / Num. obs: 18972 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 5.4 % / Biso Wilson estimate: 53.63 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.8
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.9 / Num. unique all: 924 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→46.978 Å / Occupancy max: 1 / Occupancy min: 0.58 / FOM work R set: 0.7644 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 28.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2706 968 5.16 %Random
Rwork0.2678 ---
all0.2679 18929 --
obs0.2679 18757 99.09 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.259 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso max: 115.36 Å2 / Biso mean: 59.1249 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--12.6119 Å2-0 Å20 Å2
2---12.6119 Å20 Å2
3---30.7127 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3574 0 0 43 3617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093612
X-RAY DIFFRACTIONf_angle_d1.1334871
X-RAY DIFFRACTIONf_chiral_restr0.075586
X-RAY DIFFRACTIONf_plane_restr0.004620
X-RAY DIFFRACTIONf_dihedral_angle_d12.6121270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.84250.33491310.372125092640100
2.8425-3.02050.35941350.34922491262699
3.0205-3.25370.28751340.324925152649100
3.2537-3.5810.33181500.28272501265199
3.581-4.09890.21491490.24382490263998
4.0989-5.16320.25761310.21682571270298
5.1632-46.98510.24961380.25972712285099

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